/*****************************************************************************
Major portions of this software are copyrighted by the Medical College
of Wisconsin, 1994-2000, and are released under the Gnu General Public
License, Version 2. See the file README.Copyright for details.
******************************************************************************/
/*
This program performs the nonparametric Friedman test for randomized
complete block design experiments.
File: 3dFriedman.c
Author: B. Douglas Ward
Date: 23 July 1997
Mod: Added changes for incorporating History notes.
Date: 08 September 1999
Mod: Replaced dataset input code with calls to THD_open_dataset,
to allow operator selection of individual sub-bricks for input.
Date: 03 December 1999
Mod: Added call to AFNI_logger.
Date: 14 March 2002
Mod: Modified routine write_afni_fict of NPstats.c so that all output
subbricks will now have the scaled short integer format.
Date: 14 March 2002
Mod: Set MAX_NAME_LENGTH equal to THD_MAX_NAME.
Date: 02 December 2002
*/
/*---------------------------------------------------------------------------*/
#define PROGRAM_NAME "3dFriedman" /* name of this program */
#define PROGRAM_AUTHOR "B. Douglas Ward" /* program author */
#define PROGRAM_INITIAL "23 July 1997" /* date of initial program release */
#define PROGRAM_LATEST "02 December 2002" /* date of latest program revision */
/*---------------------------------------------------------------------------*/
#include <stdio.h>
#include <math.h>
#include "mrilib.h"
#define MAX_TREATMENTS 100 /* max. number of treatments */
#define MAX_OBSERVATIONS 100 /* max. number of observations per treatment */
#define MAX_NAME_LENGTH THD_MAX_NAME /* max. string length for file names */
#define MEGA 1048576 /* one megabyte */
typedef struct NP_options
{
int datum; /* data type for "intensity" data subbrick */
char session[MAX_NAME_LENGTH]; /* name of output directory */
int nvoxel; /* number of voxel for special output */
int s; /* number of treatments */
int n[MAX_TREATMENTS]; /* number of observations per treatment */
char *** xname; /* names of the input data files */
char * first_dataset; /* name of the first data set */
int nx, ny, nz; /* data set dimensions */
int nxyz; /* number of voxels per image */
int workmem; /* working memory */
char * outfile; /* name of output file */
} NP_options;
#include "NPstats.c"
/*---------------------------------------------------------------------------*/
/*
Routine to display 3dFriedman help menu.
*/
void display_help_menu()
{
printf
(
"This program performs nonparametric Friedman test for \n"
"randomized complete block design experiments. \n\n"
"Usage: \n"
"3dFriedman \n"
"-levels s s = number of treatments \n"
"-dset 1 filename data set for treatment #1 \n"
" . . . . . . \n"
"-dset 1 filename data set for treatment #1 \n"
" . . . . . . \n"
"-dset s filename data set for treatment #s \n"
" . . . . . . \n"
"-dset s filename data set for treatment #s \n"
" \n"
"[-workmem mega] number of megabytes of RAM to use \n"
" for statistical workspace \n"
"[-voxel num] screen output for voxel # num \n"
"-out prefixname Friedman statistics are written \n"
" to file prefixname \n"
"\n");
printf
(
"\n"
"N.B.: For this program, the user must specify 1 and only 1 sub-brick \n"
" with each -dset command. That is, if an input dataset contains \n"
" more than 1 sub-brick, a sub-brick selector must be used, e.g.: \n"
" -dset 2 'fred+orig[3]' \n"
);
printf("\n" MASTER_SHORTHELP_STRING ) ;
exit(0);
}
/*---------------------------------------------------------------------------*/
/*
Routine to initialize input options.
*/
void initialize_options (NP_options * option_data)
{
int i; /* index */
option_data->datum = ILLEGAL_TYPE;
strcpy (option_data->session, "./");
option_data->nvoxel = -1;
option_data->s = 0;
for (i = 0; i < MAX_TREATMENTS; i++)
option_data->n[i] = 0;
option_data->workmem = 12;
/*----- allocate memory for storing data file names -----*/
option_data->xname = (char ***) malloc (sizeof(char **) * MAX_TREATMENTS);
for (i = 0; i < MAX_TREATMENTS; i++)
option_data->xname[i]
= (char **) malloc (sizeof(char *) * MAX_OBSERVATIONS);
option_data->first_dataset = NULL;
option_data->nx = 0;
option_data->ny = 0;
option_data->nz = 0;
option_data->nxyz = 0;
option_data->outfile = NULL;
}
/*---------------------------------------------------------------------------*/
/*
Routine to get user specified Friedman options.
*/
void get_options (int argc, char ** argv, NP_options * option_data)
{
int nopt = 1; /* input option argument counter */
int ival; /* integer input */
int nijk; /* count of data files */
float fval; /* float input */
THD_3dim_dataset * dset=NULL; /* test whether data set exists */
char message[MAX_NAME_LENGTH]; /* error message */
/*----- does user request help menu? -----*/
if (argc < 2 || strncmp(argv[1], "-help", 5) == 0) display_help_menu();
/*----- add to program log -----*/
AFNI_logger (PROGRAM_NAME,argc,argv);
/*----- initialize the input options -----*/
initialize_options (option_data);
/*----- main loop over input options -----*/
while (nopt < argc)
{
/*----- -datum type -----*/
if( strncmp(argv[nopt],"-datum",6) == 0 ){
if( ++nopt >= argc ) NP_error("need an argument after -datum!") ;
if( strcmp(argv[nopt],"short") == 0 ){
option_data->datum = MRI_short ;
} else if( strcmp(argv[nopt],"float") == 0 ){
option_data->datum = MRI_float ;
} else {
char buf[256] ;
sprintf(buf,
"-datum of type '%s' is not supported in 3dFriedman.",
argv[nopt] ) ;
NP_error(buf) ;
}
nopt++ ; continue ; /* go to next arg */
}
/*----- -session dirname -----*/
if( strncmp(argv[nopt],"-session",6) == 0 ){
nopt++ ;
if( nopt >= argc ) NP_error("need argument after -session!") ;
strcpy(option_data->session , argv[nopt++]) ;
continue ;
}
/*----- -voxel num -----*/
if (strncmp(argv[nopt], "-voxel", 6) == 0)
{
nopt++;
if (nopt >= argc) NP_error ("need argument after -voxel ");
sscanf (argv[nopt], "%d", &ival);
if (ival <= 0)
NP_error ("illegal argument after -voxel ");
option_data->nvoxel = ival;
nopt++;
continue;
}
/*----- -workmem megabytes -----*/
if( strncmp(argv[nopt],"-workmem",6) == 0 ){
nopt++ ;
if( nopt >= argc ) NP_error ("need argument after -workmem!") ;
sscanf (argv[nopt], "%d", &ival);
if( ival <= 0 ) NP_error ("illegal argument after -workmem!") ;
option_data->workmem = ival ;
nopt++ ; continue ;
}
/*----- -levels s -----*/
if (strncmp(argv[nopt], "-levels", 7) == 0)
{
nopt++;
if (nopt >= argc) NP_error ("need argument after -levels ");
sscanf (argv[nopt], "%d", &ival);
if ((ival <= 0) || (ival > MAX_TREATMENTS))
NP_error ("illegal argument after -levels ");
option_data->s = ival;
nopt++;
continue;
}
/*----- -dset level filename -----*/
if (strncmp(argv[nopt], "-dset", 5) == 0)
{
nopt++;
if (nopt+1 >= argc) NP_error ("need 2 arguments after -dset ");
sscanf (argv[nopt], "%d", &ival);
if ((ival <= 0) || (ival > option_data->s))
NP_error ("illegal argument after -dset ");
option_data->n[ival-1] += 1;
if (option_data->n[ival-1] > MAX_OBSERVATIONS)
NP_error ("too many data files");
nijk = option_data->n[ival-1];
/*--- check whether input files exist ---*/
nopt++;
dset = THD_open_dataset( argv[nopt] ) ;
CHECK_OPEN_ERROR(dset,argv[nopt]) ;
/*--- check number of selected sub-bricks ---*/
if (DSET_NVALS(dset) != 1)
{
sprintf(message,"Must specify exactly 1 sub-brick for file %s\n",
argv[nopt]);
NP_error (message);
}
THD_delete_3dim_dataset( dset , False ) ; dset = NULL ;
option_data->xname[ival-1][nijk-1]
= malloc (sizeof(char) * MAX_NAME_LENGTH);
strcpy (option_data->xname[ival-1][nijk-1], argv[nopt]);
nopt++;
continue;
}
/*----- -out filename -----*/
if (strncmp(argv[nopt], "-out", 4) == 0)
{
nopt++;
if (nopt >= argc) NP_error ("need argument after -out ");
option_data->outfile = malloc (sizeof(char) * MAX_NAME_LENGTH);
strcpy (option_data->outfile, argv[nopt]);
nopt++;
continue;
}
/*----- unknown command -----*/
NP_error ("unrecognized command line option ");
}
}
/*---------------------------------------------------------------------------*/
/*
Routine to check for valid inputs.
*/
void check_for_valid_inputs (NP_options * option_data)
{
int i, n;
char message[MAX_NAME_LENGTH]; /* error message */
n = option_data->n[0];
if (n < 1)
NP_error ("Sample size is too small");
for (i = 1; i < option_data->s; i++)
if (option_data->n[i] != n)
NP_error ("Must have equal sample sizes for all treatments");
if (option_data->nvoxel > option_data->nxyz)
NP_error ("argument of -voxel is too large");
}
/*---------------------------------------------------------------------------*/
/*
Routine to perform all Friedman initialization.
*/
void initialize
(
int argc, /* number of input arguments */
char ** argv, /* array of input arguments */
NP_options ** option_data, /* user input options */
float ** best, /* index of best treatment */
float ** qstat /* Friedman statistic */
)
{
/*----- allocate memory space for input data -----*/
*option_data = (NP_options *) malloc(sizeof(NP_options));
if (*option_data == NULL)
NP_error ("memory allocation error");
/*----- get command line inputs -----*/
get_options(argc, argv, *option_data);
/*----- use first data set to get data set dimensions -----*/
(*option_data)->first_dataset = (*option_data)->xname[0][0];
get_dimensions (*option_data);
printf ("Data set dimensions: nx = %d ny = %d nz = %d nxyz = %d \n",
(*option_data)->nx, (*option_data)->ny,
(*option_data)->nz, (*option_data)->nxyz);
/*----- check for valid inputs -----*/
check_for_valid_inputs (*option_data);
/*----- check whether output files already exist -----*/
if( THD_deathcon() ) check_one_output_file (*option_data, (*option_data)->outfile);
/*----- allocate memory -----*/
*best = (float *) malloc(sizeof(float) * (*option_data)->nxyz);
if (*best == NULL)
NP_error ("memory allocation error");
*qstat = (float *) malloc(sizeof(float) * (*option_data)->nxyz);
if (*qstat == NULL)
NP_error ("memory allocation error");
}
/*---------------------------------------------------------------------------*/
/*
Calculate the Friedman statistic.
*/
void calc_stat
(
int nvox, /* flag for voxel output */
int s, /* number of treatments */
int n, /* number of observations per treatment */
float ** xarray, /* array of data arrays */
float * best, /* index of best treatment */
float * qstat /* Friedman statistic */
)
{
const float EPSILON = 1.0e-10; /* protection from roundoff error */
int i, j; /* array indices */
node * head = NULL; /* points to head of list */
node * ptr = NULL; /* points to current position in list */
int NN; /* total number of sample points */
float rsum; /* sum of squares of ranks */
int d; /* count of number of ties */
float corr; /* correction to account for ties */
float rank; /* rank of data point */
float ranksum; /* sum of ranks for ith treatment */
float qnum; /* numerator of Friedman statistic */
float qden; /* denominator of Friedman statistic */
float best_rank; /* best average rank for a treatment */
float ** rank_array; /* array to store ranks for all observations */
/*----- allocate memory for storing ranks -----*/
rank_array = (float **) malloc (sizeof(float *) * s);
for (i = 0; i < s; i++)
rank_array[i] = (float *) malloc (sizeof(float) * n);
/*----- loop over blocks -----*/
corr = 0.0;
for (j = 0; j < n; j++)
{
/*----- enter and sort data for each treatment within block j -----*/
for (i = 0; i < s; i++)
node_addvalue (&head, xarray[i][j]);
/*----- store the ranks for each treatment within block j -----*/
for (i = 0; i < s; i++)
rank_array[i][j] = node_get_rank (head, xarray[i][j]);
/*----- calculate the ties correction factor -----*/
ptr = head;
while (ptr != NULL)
{
d = ptr->d;
corr += d*d*d - d;
ptr = ptr->next;
}
list_delete (&head);
} /* j loop */
/*----- if display voxel, write the ranks of the input data -----*/
if (nvox > 0)
{
printf ("\n");
for (i = 0; i < s; i++)
{
printf ("Y%d ranks: ", i+1);
for (j = 0; j < n; j++)
{
rank = rank_array[i][j];
printf (" %6.1f", rank);
if (((j+1) % 8 == 0) && (j < n-1))
printf ("\n ");
}
printf ("\n");
if (n > 8) printf ("\n");
}
printf ("\n");
for (i = 0; i < s; i++)
{
printf ("Y%d: ", i+1);
ranksum = 0.0;
for (j = 0; j < n; j++)
{
rank = rank_array[i][j];
ranksum += rank;
}
printf (" Rank sum = %6.1f Rank average = %6.1f \n",
ranksum, ranksum/n);
}
printf ("\n");
}
/*----- calculate the sum of the ranks -----*/
rsum = 0.0;
*best = 0.0;
best_rank = (s + 1.0) / 2.0 + EPSILON;
for (i = 0; i < s; i++)
{
ranksum = 0.0;
for (j = 0; j < n; j++)
ranksum += rank_array[i][j];
rsum += ranksum * ranksum;
if (ranksum/n > best_rank)
{
*best = (float) (i+1);
best_rank = ranksum / n;
}
}
/*----- numerator of Friedman statistic -----*/
qnum = (12.0/(n*s*(s+1)))*rsum - 3.0*n*(s+1);
/*----- denominator of Friedman statistic -----*/
qden = 1.0 - (corr / (n*s*(s*s-1)));
/*----- calculate Friedman statistic -----*/
if (qden < EPSILON)
*qstat = 0.0;
else
*qstat = qnum / qden;
if (nvox > 0) printf ("Q = %f \n", *qstat);
/*----- deallocate memory -----*/
for (i = 0; i < s; i++)
{
free (rank_array[i]);
rank_array[i] = NULL;
}
free (rank_array);
rank_array = NULL;
}
/*---------------------------------------------------------------------------*/
/*
Calculate results for a single voxel.
*/
void process_voxel
(
int nvox, /* flag for voxel output */
int s, /* number of treatments */
int n, /* number of observations per treatment */
float ** xarray, /* array of data arrays */
float * best, /* index of best treatment */
float * qstat /* Friedman statistic */
)
{
int i; /* treatment index */
int j; /* array index */
/*----- check for voxel output -----*/
if (nvox > 0)
{
printf ("\nResults for voxel #%d : \n\n", nvox);
for (i = 0; i < s; i++)
{
printf ("Y%d data: ", i+1);
for (j = 0; j < n; j++)
{
printf (" %6.1f", xarray[i][j]);
if (((j+1) % 8 == 0) && (j < n-1))
printf ("\n ");
}
printf ("\n");
if (n > 8) printf ("\n");
}
if (n <= 8) printf ("\n");
}
/*----- calculate Friedman statistic -----*/
calc_stat (nvox, s, n, xarray, best, qstat);
}
/*---------------------------------------------------------------------------*/
/*
Calculate the Friedman statistics for all voxels (by breaking the datasets
into sub-volumes, if necessary).
*/
void calculate_results
(
NP_options * option_data, /* user input options */
float * best, /* index of best treatment */
float * qstat /* Friedman statistics */
)
{
int i, j, m; /* array indices */
int s; /* number of treatments */
int n; /* number of observations per treatment */
int nxyz; /* number of voxels per dataset */
int num_datasets; /* total number of datasets */
int piece_size; /* number of voxels in dataset sub-volume */
int num_pieces; /* dataset is divided into this many pieces */
int piece; /* piece index */
int piece_len; /* number of voxels in current sub-volume */
int fim_offset; /* array offset to current sub-volume */
int ivox; /* index to voxels in current sub-volume */
int nvox; /* index of voxel within entire volume */
float b; /* index of best treatment */
float q; /* Friedman statistic */
float ** xfimar; /* array of sub-volumes of datasets */
float ** xarray; /* array of data arrays */
/*----- initialize local variables -----*/
s = option_data->s;
nxyz = option_data->nxyz;
num_datasets = 0;
n = option_data->n[0];
num_datasets = n * s;
/*----- break problem into smaller pieces -----*/
piece_size = option_data->workmem * MEGA / (num_datasets * sizeof(float));
if (piece_size > nxyz) piece_size = nxyz;
num_pieces = (nxyz + piece_size - 1) / piece_size;
printf ("num_pieces = %d piece_size = %d \n", num_pieces, piece_size);
/*----- allocate memory space -----*/
xarray = (float **) malloc (sizeof(float *) * s); MTEST(xarray);
for (i = 0; i < s; i++)
{
xarray[i] = (float *) malloc (sizeof(float) * option_data->n[i]);
MTEST(xarray[i]);
}
xfimar = (float **) malloc (sizeof(float *) * num_datasets); MTEST(xfimar);
for (i = 0; i < num_datasets; i++)
{
xfimar[i] = (float *) malloc (sizeof(float) * piece_size);
MTEST(xfimar[i]);
}
/*----- loop over the pieces of the input datasets -----*/
nvox = 0;
for (piece = 0; piece < num_pieces; piece++)
{
printf ("piece = %d \n", piece);
fim_offset = piece * piece_size;
if (piece < num_pieces-1)
piece_len = piece_size;
else
piece_len = nxyz - fim_offset;
/*----- read in sub-volume of data from each dataset -----*/
m = 0;
for (i = 0; i < s; i++)
for (j = 0; j < option_data->n[i]; j++)
{
read_afni_data (option_data, option_data->xname[i][j],
piece_len, fim_offset, xfimar[m]);
m++;
}
/*----- loop over voxels in this piece -----*/
for (ivox = 0; ivox < piece_len; ivox++)
{
nvox += 1;
m = 0;
for (i = 0; i < s; i++)
for (j = 0; j < option_data->n[i]; j++)
{
xarray[i][j] = xfimar[m][ivox];
m++;
}
/*----- calculate results for this voxel -----*/
if (nvox == option_data->nvoxel)
process_voxel (nvox, s, n, xarray, &b, &q);
else
process_voxel (-1, s, n, xarray, &b, &q);
/*----- save results for this voxel -----*/
best[ivox+fim_offset] = b;
qstat[ivox+fim_offset] = q;
}
} /* loop over pieces */
/*----- deallocate memory -----*/
for (i = 0; i < s; i++)
{
free (xarray[i]); xarray[i] = NULL;
}
free (xarray); xarray = NULL;
for (i = 0; i < num_datasets; i++)
{
free (xfimar[i]); xfimar[i] = NULL;
}
free (xfimar); xfimar = NULL;
}
/*---------------------------------------------------------------------------*/
/*
Generate the requested output.
*/
void output_results
(
int argc, /* number of input arguments */
char ** argv, /* array of input arguments */
NP_options * option_data, /* user input options */
float * best, /* index of best treatment */
float * qstat /* Friedman statistic */
)
{
/*----- write out afni fict data file -----*/
write_afni_fict (argc, argv, option_data, option_data->outfile,
best, qstat, option_data->s - 1);
}
/*---------------------------------------------------------------------------*/
/*
Routine to release memory and remove any remaining temporary data files.
*/
void terminate
(
NP_options ** option_data, /* user input options */
float ** best, /* index of best treatment */
float ** qstat /* Friedman statistics */
)
{
int i, j; /* dataset indices */
/*----- deallocate memory -----*/
for (i = 0; i < (*option_data)->s; i++)
for (j = 0; j < (*option_data)->n[i]; j++)
{
free ((*option_data)->xname[i][j]);
(*option_data)->xname[i][j] = NULL;
}
for (i = 0; i < (*option_data)->s; i++)
{
free ((*option_data)->xname[i]);
(*option_data)->xname[i] = NULL;
}
free ((*option_data)->xname);
(*option_data)->xname = NULL;
if ((*option_data)->outfile != NULL)
{
free ((*option_data)-> outfile);
(*option_data)->outfile = NULL;
}
free (*option_data); *option_data = NULL;
free (*best); *best = NULL;
free (*qstat); *qstat = NULL;
}
/*---------------------------------------------------------------------------*/
/*
Perform nonparametric Friedman test for comparison of multiple
treatments.
*/
int main (int argc, char ** argv)
{
NP_options * option_data = NULL; /* user input options */
float * best; /* index of best treatment */
float * qstat; /* Friedman statistic */
/*----- Identify software -----*/
#if 0
printf ("\n\n");
printf ("Program: %s \n", PROGRAM_NAME);
printf ("Author: %s \n", PROGRAM_AUTHOR);
printf ("Initial Release: %s \n", PROGRAM_INITIAL);
printf ("Latest Revision: %s \n", PROGRAM_LATEST);
printf ("\n");
#endif
PRINT_VERSION("3dFriedman") ; AUTHOR(PROGRAM_AUTHOR); mainENTRY("3dFriedman main") ; machdep() ;
/*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/
{ int new_argc ; char ** new_argv ;
addto_args( argc , argv , &new_argc , &new_argv ) ;
if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; }
}
/*----- program initialization -----*/
initialize (argc, argv, &option_data, &best, &qstat);
/*----- calculate nonparameteric Friedman statistics -----*/
calculate_results (option_data, best, qstat);
/*----- generate requested output -----*/
output_results (argc, argv, option_data, best, qstat);
/*----- terminate program -----*/
terminate (&option_data, &best, &qstat);
}
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